Re: [Rd] R CMD build now removes empty dirs

From: Martin Maechler <maechler_at_stat.math.ethz.ch>
Date: Mon, 11 Apr 2011 12:00:04 +0200

>>>>> Pages, Herve <hpages_at_fhcrc.org>
>>>>> on Tue, 29 Mar 2011 23:56:47 -0700 (PDT) writes:

> Hi, It's unfortunate that with recent revisions of R 2.13
> (this appeared in revision 54640, March 2), 'R CMD build'
> now removes empty dirs in the package. People might have
> good reasons for having empty dirs in their packages. For
> example, in Bioconductor, we have some tools to
> automatically generate annotation packages and those tools
> are implemented in software packages that use templates
> for the annotation packages to be generated. Those package
> templates are stored under the inst/ folder of the
> software package. One of those software packages is the
> AnnotationDbi package: it contains 41 package templates
> under inst/:

> [hpages@latitude Rpacks]$ ls
> AnnotationDbi/inst/AnnDbPkg-templates/ AFFYHUEX.DB
> CHIMP.DB MALARIA.DB WORM.DB ANOPHELES.DB COELICOLOR.DB
> MOUSECHIP.DB XENOPUSCHIP.DB ARABIDOPSISCHIP.DB
> ECOLICHIP.DB MOUSE.DB XENOPUS.DB ARABIDOPSIS.DB ECOLI.DB
> ORGANISM.DB YEASTCHIP.DB BASEPKG.DB FLYCHIP.DB PFAM.DB
> YEAST.DB BOVINECHIP.DB FLY.DB PIGCHIP.DB YEASTNCBI.DB
> BOVINE.DB GO.DB PIG.DB ZEBRAFISHCHIP.DB CANINECHIP.DB
> HUMANCHIP.DB RATCHIP.DB ZEBRAFISH.DB CANINE.DB HUMAN.DB
> RAT.DB CHICKENCHIP.DB INPARANOID.DB RHESUS.DB CHICKEN.DB
> KEGG.DB WORMCHIP.DB

> Those package templates are just the skeletons of the
> hundreds of annotation packages that we generate. Of
> course, each of them contains empty subfolders.

> Having 'R CMD build' remove those empty subfolders breaks
> all the tools that make use of those package templates.
 

> Maybe I've missed it but I didn't see any mention of this
> "feature" on this list and the fact that it was added only
> 6 weeks before the next R and Bioconductor releases is
> only making this worse.

> I hope this "feature" can be reverted. Why would people or
> our build system need to start using R CMD build
> --keep-empty-dirs just to get a source tarball right?

> Thanks, H.

> PS: This page

> http://stat.ethz.ch/R-manual/R-devel/doc/html/NEWS.html

> (referenced from http://developer.r-project.org/) has not
> been updated for months.

Thank you, Herve.
I've only now read your e-mail.
(and I now also agree that --keep-empty-dirs should *not* be needed  to keep an empty inst/ !)

Thanks for the heads up about NEWS.html. It's finally current again, and hopefully remains so: It got outdated accidentally, as it was removed from the default 'make' target, and now needs an extra make call.

Martin Maechler, ETH Zurich



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